gatk-3.8/archive/java/src/org/broadinstitute/sting/annotations/QualityAdjustedSecondBaseLod.java

package org.broadinstitute.sting.gatk.walkers.annotator;

import org.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;

import java.util.Map;
import java.util.HashMap;
import java.util.List;
import java.util.Arrays;

public class QualityAdjustedSecondBaseLod implements InfoFieldAnnotation, ExperimentalAnnotation {
    private final String KEY_NAME = "Qual_Adjusted_2blod";
    private final double CHI_LOD_MAX = -1000.0;
    private final SecondBaseSkew skewCalc = new SecondBaseSkew();
    private final double log10e = Math.log10(Math.E);
    private final double log10half = Math.log10(1.0/2);

    public List<String> getKeyNames() { return Arrays.asList(KEY_NAME); }

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(KEY_NAME, 1, VCFHeaderLineType.Float, "Adjusted residual quality based on second-base skew")); }
    
    public Map<String, Object> annotate( RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> contexts, VariantContext vc) {
        String chi = skewCalc.getAnnotation(ref, contexts, vc);
        if ( chi == null )
            return null;
        double chi_square = Double.valueOf(chi);
        double chi_loglik = chi_square <= 0.0 ? 0.0 : Math.max(-(chi_square/2.0)*log10e + log10half,CHI_LOD_MAX); // cap it...
        Map<String, Object> map = new HashMap<String, Object>();
        map.put(getKeyNames().get(0), String.format("%f", 10*(vc.getNegLog10PError() + chi_loglik)));
        return map;
    }
}